Poxviruses provide a unique experimental system for studying DNA replication. Required enzymes and factors are encoded within the viral genome and DNA synthesis and processing occurs within the cytoplasmic compartment of the cell. Analysis of a large series of temperature sensitive mutants of vaccinia virus has allowed us to divide genome formation into two stages: DNA replication which generates concatemers and resolution of concatemers into monomers. Expression of early genes is required for the former and late genes for the latter. Site-directed mutagenesis was used to define the sequence required for the resolution of the vaccinia virus concatemer junction. A model for resolution involving site- specific recombination and oriented branch migration is consistent with our data. The requirements for resolution and intramolecular recombination are different. Biochemical and genetic studies indicated that early functions including DNA replication are necessary for intramolecular recombination in transfected plasmids but that late functions are not necessary. A DNA+ temperature sensitive mutant blocked in recombination was found.